Leukocyte immunoglobulin-like receptor (LILR) B3 and LILRA6 represent a pair of inhibitory/activating receptors with identical extracellular domains and unknown ligands. LILRB3 can mediate inhibitory signaling via immunoreceptor tyrosine-based inhibition motifs (ITIMs) in its cytoplasmic tail whereas LILRA6 can signal through association with an activating adaptor molecule, FcRgamma, which bears a cytoplasmic tail with an immunoreceptor tyrosine-based activation motif (ITAM). The receptors are encoded by two highly polymorphic neighboring genes within the Leukocyte Receptor Complex (LRC) on human chromosome 19. We undertook a comprehensive genetic analysis of the LILRB3/A6 locus and investigated gene-specific expression. The data confirm the presence of high levels of non-synonymous variation in both genes with the majority of polymorphic sites being identical. In addition, the LILRA6 gene exhibits copy number variation (CNV) whereas LILRB3 does not. A screen of healthy Caucasians indicated that 32% of the subjects possessed more than 2 copies of LILRA6, whereas 4% have only one copy of the gene per diploid genome. Thus it is apparent that this locus has been subjected to non-allelic homologous recombination (NAHR) over time, resulting in variable copy numbers of the activating LILRA6 gene, but maintenance of a single fixed copy of the inhibitory LILRB3 gene.. Analysis of mRNA expression in the major fractions of PBMCs showed that LILRA6 is primarily expressed in monocytes, similarly to LILRB3, and its expression level correlates with copy number of the gene. We suggest that the LILRA6 CNV may influence the level of the activating receptor on the cell surface, potentially affecting signaling upon LILRB3/A6 ligation. The human KIR genes are arranged in at least six major gene-content haplotypes, all of which are combinations of four centromeric and two telomeric motifs. Several less frequent or minor haplotypes also exist, including insertions, deletions, and hybridization of KIR genes derived from the major haplotypes. These haplotype structures and their concomitant linkage disequilibrium among KIR genes suggest that more meaningful correlative data from studies of KIR genetics and complex disease may be achieved by measuring haplotypes of the KIR region in total. Previous studies of the KIR region have yielded detailed information about KIR haplotype structures derived uniquely from complete phased genomic sequences, revealing substructures of known haplotypes and further defined linkage among the KIR genes. Taking into account the many reported correlations between KIR polymorphism and disease, there is some imperative to incorporate KIR haplotype structures, including potential intraregion epistasis, into the association studies so that causative variation at KIR can be identified. In addition, the repetitive gene content structure of the KIR region may contribute to rapid evolution through aberrant recombination mechanisms, possibly driven by the immune function of KIR and providing further impetus towards understanding overall genomic region variation. Towards that end, a KIR haplotyping method developed by our collaborators that reports unambiguous combinations of KIR gene-content haplotypes, including both phase and copy number for each KIR was utilized. A total of 37 different gene content haplotypes were detected from 4,512 individuals and new sequence data was derived from haplotypes where the detailed structure was not previously available. An additional 10 haplotypes were detected in single copy but were not confirmed by sequencing. The 37 KIR haplotypes were sorted into 10 types of structural alterations, including gene deletions, insertions, and hybridizations, which together suggest a number of recombination events that might have occurred during KIR evolution. These new structures suggest a number of specific recombinant events during the course of KIR evolution, and add to an expanding diversity ofpotential new KIR haplotypes derived from gene duplication, deletion, and hybridization. The data provide important information regarding KIR genetic factors that may contribute to disease outcome.